Bio/Restriction/IO.pm

   1 #
   2 # BioPerl module for Bio::Restriction::IO
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Rob Edwards <redwards@utmem.edu>
   7 #
   8 # Copyright Rob Edwards
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Restriction::IO - Handler for sequence variation IO Formats
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Restriction::IO;
  21
  22     $in  = Bio::Restriction::IO->new(-file => "inputfilename" ,
  23                                      -format => 'withrefm');
  24     my $res = $in->read; # a Bio::Restriction::EnzymeCollection
  25
  26 =head1 DESCRIPTION
  27
  28 L<Bio::Restriction::IO> is a handler module for the formats in the
  29 Restriction IO set, e.g. C<Bio::Restriction::IO::xxx>. It is the
  30 officially sanctioned way of getting at the format objects, which most
  31 people should use.
  32
  33 The structure, conventions and most of the code is inherited from
  34 L<Bio::SeqIO>. The main difference is that instead of using methods
  35 C<next_seq>, you drop C<_seq> from the method name.
  36
  37 Also, instead of dealing only with individual L<Bio::Restriction::Enzyme>
  38 objects, C<read()> will slurp in all enzymes into a
  39 L<Bio::Restriction::EnzymeCollection> object.
  40
  41 For more details, see documentation in L<Bio::SeqIO>.
  42
  43 =head1 TO DO
  44
  45 At the moment, these can be use mainly to get a custom set if enzymes in
  46 C<withrefm> or C<itype2> formats into L<Bio::Restriction::Enzyme> or
  47 L<Bio::Restriction::EnzymeCollection> objects.  Using C<bairoch> format is
  48 highly experimental and is not recommmended at this time.
  49
  50 This class inherits from L<Bio::SeqIO> for convenience sake, though this should
  51 inherit from L<Bio::Root::Root>.  Get rid of L<Bio::SeqIO> inheritance by
  52 copying relevant methods in.
  53
  54 C<write()> methods are currently not implemented for any format except C<base>.
  55 Using C<write()> even with C<base> format is not recommended as it does not
  56 support multicut/multisite enzyme output.
  57
  58 Should additional formats be supported (such as XML)?
  59
  60 =head1 SEE ALSO
  61
  62 L<Bio::SeqIO>,
  63 L<Bio::Restriction::Enzyme>,
  64 L<Bio::Restriction::EnzymeCollection>
  65
  66 =head1 FEEDBACK
  67
  68 =head2 Mailing Lists
  69
  70 User feedback is an integral part of the evolution of this and other
  71 Bioperl modules. Send your comments and suggestions preferably to the
  72 Bioperl mailing lists Your participation is much appreciated.
  73
  74   bioperl-l@bioperl.org                  - General discussion
  75   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  76
  77 =head2 Support
  78
  79 Please direct usage questions or support issues to the mailing list:
  80
  81 I<bioperl-l@bioperl.org>
  82
  83 rather than to the module maintainer directly. Many experienced and
  84 reponsive experts will be able look at the problem and quickly
  85 address it. Please include a thorough description of the problem
  86 with code and data examples if at all possible.
  87
  88 =head2 Reporting Bugs
  89
  90 report bugs to the Bioperl bug tracking system to help us keep track
  91 the bugs and their resolution.  Bug reports can be submitted via the
  92 web:
  93
  94   https://github.com/bioperl/bioperl-live/issues
  95
  96 =head1 AUTHOR
  97
  98 Rob Edwards, redwards@utmem.edu
  99
 100 =head1 CONTRIBUTORS
 101
 102 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
 103
 104 =head1 APPENDIX
 105
 106 The rest of the documentation details each of the object
 107 methods. Internal methods are usually preceded with a _
 108
 109 =cut
 110
 111 # Let the code begin...
 112
 113 package Bio::Restriction::IO;
 114
 115 use strict;
 116 use vars qw(%FORMAT);
 117 use base qw(Bio::SeqIO);
 118
 119 %FORMAT = (
 120             'itype2'    => 'itype2',
 121             '8'         => 'itype2',
 122             'withrefm'  => 'withrefm',
 123             '31'        => 'withrefm',
 124             'base'      => 'base',
 125             '0'         => 'base',
 126             'bairoch'   => 'bairoch',
 127             '19'        => 'bairoch',
 128             'macvector' => 'bairoch',
 129             'vectorNTI' => 'bairoch',
 130             'neo'       => 'prototype',
 131             'prototype' => 'prototype'
 132 );
 133
 134 =head2 new
 135
 136  Title   : new
 137  Usage   : $stream = Bio::Restriction::IO->new(-file => $filename,
 138                                                -format => 'Format')
 139  Function: Returns a new seqstream
 140  Returns : A Bio::Restriction::IO::Handler initialised with
 141            the appropriate format
 142  Args    : -file => $filename
 143            -format => format
 144            -fh => filehandle to attach to
 145
 146 =cut
 147
 148 sub new {
 149    my ($class, %param) = @_;
 150    my ($format);
 151
 152    @param{ map { lc $_ } keys %param } = values %param;  # lowercase keys
 153    $format = $FORMAT{$param{'-format'}} if defined $param{'-format'};
 154    $format ||= $class->_guess_format( $param{-file} || $ARGV[0] )
 155              || 'base';
 156    $format = "\L$format"; # normalize capitalization to lower case
 157
 158    return unless $class->_load_format_module($format);
 159    return "Bio::Restriction::IO::$format"->new(%param);
 160 }
 161
 162
 163 =head2 format
 164
 165  Title   : format
 166  Usage   : $format = $stream->format()
 167  Function: Get the restriction format
 168  Returns : restriction format
 169  Args    : none
 170
 171 =cut
 172
 173 # format() method inherited from Bio::Root::IO
 174
 175
 176 sub _load_format_module {
 177   my ($class, $format) = @_;
 178   my $module = "Bio::Restriction::IO::" . $format;
 179   my $ok;
 180   eval {
 181       $ok = $class->_load_module($module);
 182   };
 183   if ( $@ ) {
 184     print STDERR <<END;
 185 $class: $format cannot be found
 186 Exception $@
 187 For more information about the IO system please see the IO docs.
 188 This includes ways of checking for formats at compile time, not run time
 189 END
 190   ;
 191   }
 192   return $ok;
 193 }
 194
 195 =head2 read
 196
 197  Title   : read
 198  Usage   : $renzs = $stream->read
 199  Function: reads all the restrction enzymes from the stream
 200  Returns : a Bio::Restriction::EnzymeCollection object
 201  Args    :
 202
 203 =cut
 204
 205 sub read {
 206    my ($self, $seq) = @_;
 207    $self->throw_not_implemented();
 208 }
 209
 210 sub next {
 211    my ($self, $seq) = @_;
 212    $self->throw_not_implemented();
 213 }
 214
 215 sub next_seq {
 216    my ($self, $seq) = @_;
 217    $self->throw_not_implemented();
 218 }
 219
 220 =head2 write
 221
 222  Title   : write
 223  Usage   : $stream->write($seq)
 224  Function: writes the $seq object into the stream
 225  Returns : 1 for success and 0 for error
 226  Args    : Bio::Restriction::EnzymeCollection object
 227
 228 =cut
 229
 230 sub write {
 231     my ($self, $seq) = @_;
 232     $self->throw("Sorry, you cannot write to a generic ".
 233                  "Bio::Restricion::IO object.");
 234 }
 235
 236 sub write_seq {
 237    my ($self, $seq) = @_;
 238    $self->warn("These are not sequence objects. ".
 239                "Use method 'write' instead of 'write_seq'.");
 240    $self->write($seq);
 241 }
 242
 243 =head2 _guess_format
 244
 245  Title   : _guess_format
 246  Usage   : $obj->_guess_format($filename)
 247  Function:
 248  Example :
 249  Returns : guessed format of filename (lower case)
 250  Args    :
 251
 252 =cut
 253
 254 sub _guess_format {
 255    my $class = shift;
 256    return  unless $_ = shift;
 257    return 'flat' if /\.dat$/i;
 258    return 'xml'  if /\.xml$/i;
 259 }
 260
 261
 262 1;